<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<html>
	<title>Annotation Options</title>
	<body style="padding:20px;width:650px;font-family:Times;">
	
	<h3>annoDB ANNOTATION:</h3>
	<table border=0 cellpadding=3>
		<tr>
			<td valign="top" nowrap>For assembled</td>
			<td>All (Contigs and Singletons), Contig Only or Singletons only, 
				where Contigs is multi-read contigs and Singleton is single-read contigs
				(this is only meaningful if an assembly was performed). 
			</td>
		</tr>
		<tr><td valign="top" nowrap>Default annodb blastx parameters
			<td>Parameters to use for blasting sequences against 
			protein databases. Parameters can also be specified for specific annoDBs in 
			the Add/Edit menus.
		<tr><td valign="top" nowrap>GO Database</td>
		<td>If you are not able to select one, then one needs to be downloaded and installed, 
		using the provided perl script newGOver.pl; see the online documentation.
		</table>
		
		<h3>SIMILAR SEQUENCES:</h3>
		If no options are selected, this step will be skipped.
		<p>
		<table border=0 cellspacing=5 cellpadding=3>
		<tr>
			<td valign="top" nowrap>Run Nucleotide Self Blast</td>
			<td>
				TCW runs the selfblast with megablast
			</td>
		</tr>
		<tr>
			<td>&nbsp;&nbsp;&nbsp;  Arguments</td>
			<td>Parameters for the megablast selfblast</td>
		</tr>
		<tr>
			<td valign="top" nowrap>Use existing</td>
			<td>The filename of a megablast selfblast file in tabular (-m8, -outfmt 6) format </td>
		</tr>
		<tr>
			<td valign="top" nowrap>Run Translated Self Blast</td>
			<td>Run the selfblast with tblastx
			</td>
		</tr>
		<tr>
			<td>&nbsp;&nbsp;&nbsp; Arguments</td>
			<td>Parameters for the tblastx selfblast </td>
		</tr>
		<tr>
			<td>Use existing</td>
			<td>The filename of a tblastx selfblast file in tabular (-m8, -outfmt 6) format</td>
		</tr>
		<tr>
			<td>Pairs limit</td>
			<td>Limits the number of pairs produced</td>
		</tr>
	</table>
</body>
</html>